Question

How fold change is calculated in Ballgown?

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Ir • 0

@ir-11113

Last seen 7.9 years ago

Hi,

I would like to clarify how Ballgown computes the fold change (FC)?

If "group" is defined as c('KO','WT'), what value goes to numerator, and what to denominator? FC= KO/WT or FC=WT/KO

pData(bg) = data.frame(id=sampleNames(bg), group=rep(c('KO', 'WT')

FC= ?

Thank you!

ballgown • 3.8k views

ADD COMMENT • link 8.0 years ago • updated 7.9 years ago Ir • 0

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Is KO & WT the covariate considered during stattest?

ADD REPLY • link 6.8 years ago Arindam ▴ 80

score 0 · Answer 1 · 2017-01-12

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Alyssa Frazee ▴ 210

@alyssa-frazee-6710

Last seen 4.1 years ago

San Francisco, CA, USA

"KO" will be used as the reference group (denominator) here, so the fold change is calculated as WT / KO.

(It's similar to the situation where you use the `lm` function in R with `group` as a covariate: KO would be the baseline factor level because it comes first alphabetically).

ADD COMMENT • link 7.9 years ago Alyssa Frazee ▴ 210

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Is any log transformation done on the FPKM values during FC calculation? I tried to manually calculate the FC by extracting the FPKM values for few genes using gexpr(), but the result I obtained differs considerably from the stattest result.

Also after stattest the genes that were supposed to be up-regulated has FC<1 and vice-versa.

ADD REPLY • link 6.8 years ago Arindam ▴ 80

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Hi Alyssa, Can you please confirming that regardless of the name of the group in the covariate, at the denominator will be always the one who comes first alphabetically,

correct?

thank you

ADD REPLY • link 5.4 years ago Merlin ▴ 10

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Hi Alyssa, Can you please confirming that regardless of the name of the group in the covariate, at the denominator will be always the one who comes first alphabetically,

correct?

thank you

ADD REPLY • link 5.4 years ago Merlin ▴ 10

score 0 · Answer 2 · 2017-01-15

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Ir • 0

@ir-11113

Last seen 7.9 years ago

Just to clarify if I missed this info in the manual, so it means that this is a default (WT/KO) and I can not control nominator and denominator ?

ADD COMMENT • link 7.9 years ago Ir • 0

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Correct: you can't control which is the numerator and which is the denominator. If you want KO in the numerator and WT in the denominator, you can take the reciprocal after doing stattest.

ADD REPLY • link 7.9 years ago Alyssa Frazee ▴ 210